Secondary structure

 Secondary structure of a protein refers to the three-dimensional structure of local segments of a protein. Each type of secondary structure has segments that have a repeating conformational pattern which is produced by a repeating pattern of values for the phi and psi torsional angles. For this reason, on a Ramachandran plot, the values for phi and psi are located at a particular area of the plot for each secondary structure.

There are three common secondary structures - helices, β-pleated sheets and turns, and there are several variations of each one of them.
 * Helices. Alpha helix, pi helix and 310 helix are the three types of helices with the alpha helix being the most important. The characteristics of these three helices are given at Helices in Proteins. Jmol colors them alpha helix, 310 helix and pi helix as shown in Helices in Proteins.


 * Strands. The strands making up the sheets can be parallel or antiparallel and the pleats in the sheet can be twisted as well as being parallel. These structural differences and other characteristics of β-sheets can be seen at Sheets in Proteins.


 * Turns. β-turn and γ-turn are the two types of turns. β-turns are composed of four amino acids and can have several difference conformations.  γ-turns are made up of only three amino acids and are therefore a much tighter turn.  More detail and illustrations of these turns are at Turns in Proteins.

The structure of a human transferrin n-lobe mutant (PDB code 1dtg) is shown in cartoon and colored structure to highlight its secondary structure, with alpha-helices in magenta and beta-sheets in yellow. Another example is domain 2 of glycogen phosphorylase (PDB code 1abb).

From PDB files
PDB files usually contain HELIX and SHEET records, in their headers. These represent the authors' determinations, and when present, Jmol obeys them (see secondary structure colors). Secondary structure assignments are somewhat arbitrary. Proteins are not rigid (unlike PDB files!), and phi/psi angles may change from instant to instant. For example, there may be an alpha helix with a small kink in the middle. Objective software may determine that this represents two alpha helices, while the authors may specify it as a single helix.

Jmol's standard color scheme for secondary structure (see Help:Color_Keys): ,,.

Jmol's objective calculation
When the PDB file lacks HELIX and SHEET records, Jmol will determine secondary structure using objective criteria. Optionally, using Jmol command language, you can re-determine secondary structure objectively, overriding the authors' specifications in the PDB file. Typically when you do this, and re-apply the Secondary Structure color scheme, some blue turns will appear. (Many PDB files used to contain TURN records, but in revision 3.2 of the PDB data format, TURN records were abolished.) ''This does not work in Jmol 11.8 employed in Proteopedia in June, 2011. It works in the Jmol/Application (version 12).'' You can run a Proteopedia page in Jmol 12.0 and observe the effect of this command by appending "?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar" to the url of the page and reloading the page. The user must give permission for the signed version of Jmol to open, and when it does it has a red frank (lower right corner), whereas in the unsigned version it is grey. Click on the Jmol frank, in the main menu which opens click on Console, in the bottom box enter the commands: select protein; calculate structure; cartoon; color structure and then click Run. See also Calculate structure.

Examples
If the above series of commands are applied when the structure of a human transferrin n-lobe mutant is displayed, you will see that in additional to the sheets and the alpha helices being displayed the 310 helices and different types of turns in blue are also shown. If the above series of commands are applied when the structure of glycogen phosphorylase (domain 2) is displayed above, all four chains will be initially displayed, but clicking the domain 2 of glycogen phosphorylase green link (above) will display only domain 2 of chain A. You will observe all three types of helices, and the turns will be colored blue. More detail on how calculate structure determines helices, strands and turns is at Calculate structure.